Classify

Name of the classified SNPs with the genotypes (required)

genotypefile

Character string specifying the directory AND name of regionsfile - e.g., "Xba.regions" (required)

regionsfile

Character string specifying the directory AND name of thetafile (required)

thetafile

Call Rate percentage; The user can specify any number from the list: 80,82,84,86,88,90,92,94,96,98,100. Default is 100%(optional)

callrate


This function entails classification of SNPs based on the theta estimates (thetafile), genotype information (A regions file), and some internal files.
Currently, this algorithm works for the Affymetrix 100K - Xba dataset.


classif

A classification algorithm, based on a multi-chip, multi-SNP
approach for Affymetrix SNP arrays. Using a large training sample where the
genotype labels are known, this aglorithm will obtain more accurate
classification results on new data. RLMM is based on a robust, linear model
and uses the Mahalanobis distance for classification. The chip-to-chip
non-biological variation is removed through normalization. This model-based
algorithm captures the similarities across genotype groups and probes, as
well as thousands other SNPs for accurate classification.
NOTE: 100K-Xba only at for now.

Nusrat Rabbee

RLMM

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Classify function

This function entails classification of SNPs based on the theta estimates (thetafile), genotype information (A regions file), and some internal files.
Currently, this algorithm works for the Affymetrix 100K - Xba dataset.

Classify: Classification of SNPs based on theta estimates

Description

Usage

Arguments

Details